Starting phenix.real_space_refine on Mon Mar 11 05:52:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vjy_21220/03_2024/6vjy_21220.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4716 2.51 5 N 1204 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7266 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 20, 'TRANS': 582} Chain breaks: 4 Time building chain proxies: 4.26, per 1000 atoms: 0.59 Number of scatterers: 7266 At special positions: 0 Unit cell: (93.79, 124.3, 123.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1312 8.00 N 1204 7.00 C 4716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 75 through 99 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 105 through 135 removed outlier: 3.537A pdb=" N ALA B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.516A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 4.071A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 296 through 324 removed outlier: 4.214A pdb=" N LEU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.829A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.637A pdb=" N PHE A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.645A pdb=" N THR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.751A pdb=" N HIS A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.518A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.630A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.604A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 315 through 331 removed outlier: 3.668A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.751A pdb=" N ASN A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.852A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.827A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.549A pdb=" N TYR A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.670A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 4.202A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 4.226A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.951A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.649A pdb=" N LYS A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.651A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.797A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 686 removed outlier: 3.862A pdb=" N THR A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2272 1.34 - 1.46: 1757 1.46 - 1.58: 3355 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7445 Sorted by residual: bond pdb=" N ARG B 294 " pdb=" CA ARG B 294 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" C ALA A 521 " pdb=" N PRO A 522 " ideal model delta sigma weight residual 1.337 1.320 0.017 1.24e-02 6.50e+03 1.84e+00 bond pdb=" C VAL B 2 " pdb=" O VAL B 2 " ideal model delta sigma weight residual 1.232 1.242 -0.011 1.01e-02 9.80e+03 1.12e+00 bond pdb=" C ASN B 153 " pdb=" O ASN B 153 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.08e-01 bond pdb=" CA ILE A 596 " pdb=" CB ILE A 596 " ideal model delta sigma weight residual 1.545 1.537 0.008 9.10e-03 1.21e+04 8.03e-01 ... (remaining 7440 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.81: 165 106.81 - 113.61: 4067 113.61 - 120.41: 2963 120.41 - 127.21: 2810 127.21 - 134.02: 73 Bond angle restraints: 10078 Sorted by residual: angle pdb=" CA ILE B 291 " pdb=" C ILE B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 120.83 117.79 3.04 6.10e-01 2.69e+00 2.49e+01 angle pdb=" O ILE B 291 " pdb=" C ILE B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 120.42 123.40 -2.98 6.40e-01 2.44e+00 2.17e+01 angle pdb=" C ASN A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C PHE B 214 " pdb=" N TYR B 215 " pdb=" CA TYR B 215 " ideal model delta sigma weight residual 120.44 124.14 -3.70 1.30e+00 5.92e-01 8.10e+00 angle pdb=" C PHE A 201 " pdb=" N ASN A 202 " pdb=" CA ASN A 202 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.05e+00 ... (remaining 10073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3925 17.78 - 35.55: 406 35.55 - 53.33: 59 53.33 - 71.11: 15 71.11 - 88.89: 3 Dihedral angle restraints: 4408 sinusoidal: 1773 harmonic: 2635 Sorted by residual: dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN A 645 " pdb=" C ASN A 645 " pdb=" N ARG A 646 " pdb=" CA ARG A 646 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA A 38 " pdb=" C ALA A 38 " pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 758 0.036 - 0.072: 280 0.072 - 0.109: 59 0.109 - 0.145: 10 0.145 - 0.181: 1 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ASP A 362 " pdb=" N ASP A 362 " pdb=" C ASP A 362 " pdb=" CB ASP A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CB VAL B 303 " pdb=" CA VAL B 303 " pdb=" CG1 VAL B 303 " pdb=" CG2 VAL B 303 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1105 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 295 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 296 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 282 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LYS B 282 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS B 282 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 283 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 27 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 28 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.020 5.00e-02 4.00e+02 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1297 2.76 - 3.29: 7787 3.29 - 3.83: 11944 3.83 - 4.36: 12907 4.36 - 4.90: 21608 Nonbonded interactions: 55543 Sorted by model distance: nonbonded pdb=" O LEU B 118 " pdb=" ND1 HIS B 122 " model vdw 2.223 2.520 nonbonded pdb=" O VAL B 25 " pdb=" OG1 THR B 29 " model vdw 2.246 2.440 nonbonded pdb=" OE2 GLU A 639 " pdb=" ND1 HIS A 640 " model vdw 2.251 2.520 nonbonded pdb=" OE1 GLN A 424 " pdb=" OH TYR A 437 " model vdw 2.297 2.440 nonbonded pdb=" O PHE B 147 " pdb=" OG SER B 151 " model vdw 2.298 2.440 ... (remaining 55538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.130 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7445 Z= 0.224 Angle : 0.641 9.861 10078 Z= 0.388 Chirality : 0.039 0.181 1108 Planarity : 0.003 0.042 1259 Dihedral : 14.400 88.885 2706 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.13 % Allowed : 5.83 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.25), residues: 869 helix: -0.34 (0.18), residues: 660 sheet: None (None), residues: 0 loop : -3.25 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 632 HIS 0.005 0.001 HIS A 661 PHE 0.018 0.001 PHE A 528 TYR 0.017 0.001 TYR A 107 ARG 0.006 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9330 (tt) cc_final: 0.8903 (mt) REVERT: B 81 HIS cc_start: 0.8819 (m170) cc_final: 0.8303 (m170) REVERT: B 125 LEU cc_start: 0.9264 (tp) cc_final: 0.9036 (mt) REVERT: B 130 GLU cc_start: 0.8918 (tp30) cc_final: 0.8542 (tm-30) REVERT: B 152 PHE cc_start: 0.7690 (t80) cc_final: 0.7376 (t80) REVERT: B 203 LEU cc_start: 0.9441 (mm) cc_final: 0.9146 (mm) REVERT: B 307 ILE cc_start: 0.6196 (mm) cc_final: 0.5664 (mm) REVERT: A 215 ARG cc_start: 0.9131 (ttm110) cc_final: 0.8898 (ttp80) REVERT: A 238 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 317 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7223 (mmp80) REVERT: A 499 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8052 (tmtt) REVERT: A 510 LYS cc_start: 0.9133 (tttt) cc_final: 0.8695 (tttp) REVERT: A 552 GLU cc_start: 0.8745 (pp20) cc_final: 0.8474 (pp20) REVERT: A 593 GLN cc_start: 0.8803 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 609 MET cc_start: 0.8575 (ttt) cc_final: 0.8139 (tmm) REVERT: A 666 TYR cc_start: 0.8388 (t80) cc_final: 0.7445 (t80) REVERT: A 670 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8554 (mptt) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1997 time to fit residues: 55.4251 Evaluate side-chains 138 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 123 ASN A 179 GLN A 186 ASN A 191 GLN A 257 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7445 Z= 0.153 Angle : 0.570 9.758 10078 Z= 0.295 Chirality : 0.037 0.197 1108 Planarity : 0.004 0.041 1259 Dihedral : 4.404 20.027 975 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.38 % Allowed : 3.42 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 869 helix: 1.27 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -2.81 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 321 HIS 0.011 0.001 HIS A 378 PHE 0.017 0.001 PHE B 214 TYR 0.021 0.001 TYR B 117 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9314 (tt) cc_final: 0.8909 (mt) REVERT: B 81 HIS cc_start: 0.8709 (m170) cc_final: 0.8505 (m170) REVERT: B 117 TYR cc_start: 0.8757 (m-80) cc_final: 0.8438 (m-80) REVERT: B 127 ASP cc_start: 0.8204 (t0) cc_final: 0.7573 (t70) REVERT: B 130 GLU cc_start: 0.8881 (tp30) cc_final: 0.8670 (tm-30) REVERT: B 152 PHE cc_start: 0.7666 (t80) cc_final: 0.7246 (t80) REVERT: B 162 TYR cc_start: 0.9236 (t80) cc_final: 0.9010 (t80) REVERT: B 307 ILE cc_start: 0.5627 (mm) cc_final: 0.5353 (mm) REVERT: A 46 GLU cc_start: 0.8644 (pm20) cc_final: 0.8214 (pm20) REVERT: A 72 LYS cc_start: 0.9291 (mttt) cc_final: 0.8721 (mptt) REVERT: A 124 MET cc_start: 0.8054 (tpt) cc_final: 0.7482 (tmm) REVERT: A 215 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8835 (ttp80) REVERT: A 217 ILE cc_start: 0.9585 (mt) cc_final: 0.9315 (tp) REVERT: A 371 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8558 (ttm110) REVERT: A 466 ILE cc_start: 0.7999 (pt) cc_final: 0.7755 (tp) REVERT: A 510 LYS cc_start: 0.9020 (tttt) cc_final: 0.8522 (tmtt) REVERT: A 532 ILE cc_start: 0.9571 (pt) cc_final: 0.9182 (mt) REVERT: A 609 MET cc_start: 0.8566 (ttt) cc_final: 0.8134 (tmm) REVERT: A 666 TYR cc_start: 0.8402 (t80) cc_final: 0.7815 (t80) outliers start: 3 outliers final: 0 residues processed: 199 average time/residue: 0.2387 time to fit residues: 61.5868 Evaluate side-chains 140 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 202 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7445 Z= 0.167 Angle : 0.547 9.517 10078 Z= 0.286 Chirality : 0.037 0.213 1108 Planarity : 0.004 0.040 1259 Dihedral : 4.242 20.080 975 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.25 % Allowed : 3.80 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 869 helix: 1.69 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -2.59 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 27 HIS 0.014 0.001 HIS B 79 PHE 0.014 0.001 PHE B 214 TYR 0.026 0.001 TYR A 153 ARG 0.009 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9323 (tt) cc_final: 0.8952 (mt) REVERT: B 117 TYR cc_start: 0.8844 (m-80) cc_final: 0.8596 (m-80) REVERT: B 127 ASP cc_start: 0.8162 (t0) cc_final: 0.7237 (t70) REVERT: B 152 PHE cc_start: 0.7645 (t80) cc_final: 0.7245 (t80) REVERT: B 162 TYR cc_start: 0.9245 (t80) cc_final: 0.9044 (t80) REVERT: A 34 LEU cc_start: 0.9193 (mt) cc_final: 0.8905 (mt) REVERT: A 72 LYS cc_start: 0.9241 (mttt) cc_final: 0.8706 (mptt) REVERT: A 124 MET cc_start: 0.8375 (tpt) cc_final: 0.7712 (tpp) REVERT: A 152 MET cc_start: 0.8121 (ttt) cc_final: 0.7880 (tpt) REVERT: A 215 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8819 (ttp80) REVERT: A 217 ILE cc_start: 0.9617 (mt) cc_final: 0.9286 (tp) REVERT: A 321 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.7821 (tmm-80) REVERT: A 466 ILE cc_start: 0.8102 (pt) cc_final: 0.7837 (tp) REVERT: A 510 LYS cc_start: 0.9029 (tttt) cc_final: 0.8553 (tmtt) REVERT: A 555 GLN cc_start: 0.9017 (mt0) cc_final: 0.8682 (mt0) REVERT: A 609 MET cc_start: 0.8577 (ttt) cc_final: 0.8118 (tmm) REVERT: A 666 TYR cc_start: 0.8385 (t80) cc_final: 0.7846 (t80) outliers start: 2 outliers final: 1 residues processed: 178 average time/residue: 0.1844 time to fit residues: 44.0579 Evaluate side-chains 132 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7445 Z= 0.236 Angle : 0.608 8.524 10078 Z= 0.318 Chirality : 0.039 0.216 1108 Planarity : 0.004 0.033 1259 Dihedral : 4.346 21.517 975 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 869 helix: 1.78 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 321 HIS 0.006 0.001 HIS B 79 PHE 0.015 0.001 PHE B 214 TYR 0.019 0.001 TYR A 74 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2129 (tpt) cc_final: 0.1673 (tpt) REVERT: B 69 LEU cc_start: 0.9385 (tt) cc_final: 0.9056 (mt) REVERT: B 117 TYR cc_start: 0.8896 (m-80) cc_final: 0.8623 (m-80) REVERT: B 127 ASP cc_start: 0.8206 (t0) cc_final: 0.7995 (t70) REVERT: B 152 PHE cc_start: 0.7623 (t80) cc_final: 0.7223 (t80) REVERT: A 34 LEU cc_start: 0.9180 (mt) cc_final: 0.8949 (mt) REVERT: A 72 LYS cc_start: 0.9256 (mttt) cc_final: 0.8756 (mptt) REVERT: A 215 ARG cc_start: 0.9122 (ttm110) cc_final: 0.8832 (ttp80) REVERT: A 217 ILE cc_start: 0.9603 (mt) cc_final: 0.9171 (tp) REVERT: A 321 ARG cc_start: 0.8551 (ptt-90) cc_final: 0.7828 (tmm-80) REVERT: A 510 LYS cc_start: 0.9034 (tttt) cc_final: 0.8604 (tmtt) REVERT: A 609 MET cc_start: 0.8586 (ttt) cc_final: 0.8134 (tmm) REVERT: A 666 TYR cc_start: 0.8448 (t80) cc_final: 0.7872 (t80) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1853 time to fit residues: 41.4416 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7445 Z= 0.151 Angle : 0.569 9.170 10078 Z= 0.291 Chirality : 0.037 0.220 1108 Planarity : 0.003 0.036 1259 Dihedral : 4.159 19.843 975 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.25 % Allowed : 1.52 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 869 helix: 1.98 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -2.27 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 321 HIS 0.004 0.001 HIS A 122 PHE 0.014 0.001 PHE B 214 TYR 0.024 0.001 TYR A 153 ARG 0.008 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9378 (tt) cc_final: 0.9160 (pp) REVERT: B 117 TYR cc_start: 0.8829 (m-10) cc_final: 0.8615 (m-80) REVERT: B 127 ASP cc_start: 0.8887 (t70) cc_final: 0.8469 (t0) REVERT: B 152 PHE cc_start: 0.7532 (t80) cc_final: 0.7188 (t80) REVERT: B 195 MET cc_start: 0.8085 (mtp) cc_final: 0.7859 (mtp) REVERT: B 215 TYR cc_start: 0.4144 (t80) cc_final: 0.3896 (t80) REVERT: A 72 LYS cc_start: 0.9309 (mttt) cc_final: 0.8820 (mptt) REVERT: A 91 GLU cc_start: 0.8893 (pt0) cc_final: 0.8627 (tp30) REVERT: A 152 MET cc_start: 0.8810 (tpp) cc_final: 0.7697 (tpt) REVERT: A 215 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8802 (ttp80) REVERT: A 418 ASP cc_start: 0.9208 (m-30) cc_final: 0.8999 (m-30) REVERT: A 441 MET cc_start: 0.8962 (tmm) cc_final: 0.8600 (tmm) REVERT: A 510 LYS cc_start: 0.9001 (tttt) cc_final: 0.8542 (tmtt) REVERT: A 520 MET cc_start: 0.8725 (mmp) cc_final: 0.8433 (mmp) REVERT: A 555 GLN cc_start: 0.9020 (mt0) cc_final: 0.8755 (mt0) REVERT: A 609 MET cc_start: 0.8486 (ttt) cc_final: 0.8080 (tmm) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.1849 time to fit residues: 44.1119 Evaluate side-chains 128 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0060 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7445 Z= 0.175 Angle : 0.581 8.443 10078 Z= 0.300 Chirality : 0.037 0.168 1108 Planarity : 0.003 0.040 1259 Dihedral : 4.156 24.511 975 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.38 % Allowed : 2.41 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 869 helix: 2.00 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.07 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 321 HIS 0.011 0.001 HIS B 79 PHE 0.017 0.001 PHE B 214 TYR 0.012 0.001 TYR A 74 ARG 0.007 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 TYR cc_start: 0.8874 (m-10) cc_final: 0.8651 (m-80) REVERT: B 127 ASP cc_start: 0.8911 (t70) cc_final: 0.8472 (t0) REVERT: B 152 PHE cc_start: 0.7467 (t80) cc_final: 0.7088 (t80) REVERT: B 215 TYR cc_start: 0.4202 (t80) cc_final: 0.3918 (t80) REVERT: A 72 LYS cc_start: 0.9230 (mttt) cc_final: 0.8730 (mmtm) REVERT: A 215 ARG cc_start: 0.9090 (ttm110) cc_final: 0.8786 (ttp80) REVERT: A 321 ARG cc_start: 0.8412 (ptt90) cc_final: 0.7879 (tmm-80) REVERT: A 418 ASP cc_start: 0.9219 (m-30) cc_final: 0.8978 (m-30) REVERT: A 441 MET cc_start: 0.8995 (tmm) cc_final: 0.8612 (tmm) REVERT: A 510 LYS cc_start: 0.9028 (tttt) cc_final: 0.8366 (tmtt) REVERT: A 514 ASP cc_start: 0.8470 (m-30) cc_final: 0.8205 (m-30) REVERT: A 555 GLN cc_start: 0.9041 (mt0) cc_final: 0.8796 (mt0) REVERT: A 609 MET cc_start: 0.8547 (ttt) cc_final: 0.8144 (tmm) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.1835 time to fit residues: 40.5086 Evaluate side-chains 126 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7445 Z= 0.147 Angle : 0.586 8.589 10078 Z= 0.295 Chirality : 0.037 0.230 1108 Planarity : 0.003 0.045 1259 Dihedral : 4.018 20.764 975 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 869 helix: 2.15 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -2.08 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 321 HIS 0.005 0.001 HIS A 122 PHE 0.014 0.001 PHE B 214 TYR 0.011 0.001 TYR A 65 ARG 0.006 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 TYR cc_start: 0.8850 (m-10) cc_final: 0.8609 (m-80) REVERT: B 127 ASP cc_start: 0.8936 (t70) cc_final: 0.8487 (t0) REVERT: B 215 TYR cc_start: 0.4178 (t80) cc_final: 0.3896 (t80) REVERT: A 72 LYS cc_start: 0.9282 (mttt) cc_final: 0.8738 (mmtm) REVERT: A 152 MET cc_start: 0.8560 (tpt) cc_final: 0.7384 (tpt) REVERT: A 215 ARG cc_start: 0.9073 (ttm110) cc_final: 0.8641 (ttp-110) REVERT: A 217 ILE cc_start: 0.9516 (mt) cc_final: 0.9229 (tp) REVERT: A 321 ARG cc_start: 0.8381 (ptt90) cc_final: 0.7826 (tmm-80) REVERT: A 418 ASP cc_start: 0.9190 (m-30) cc_final: 0.8953 (m-30) REVERT: A 441 MET cc_start: 0.9018 (tmm) cc_final: 0.8632 (tmm) REVERT: A 510 LYS cc_start: 0.9009 (tttt) cc_final: 0.8311 (tmtt) REVERT: A 514 ASP cc_start: 0.8402 (m-30) cc_final: 0.8145 (m-30) REVERT: A 520 MET cc_start: 0.8541 (mmp) cc_final: 0.8242 (mmm) REVERT: A 609 MET cc_start: 0.8534 (ttt) cc_final: 0.8098 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1831 time to fit residues: 40.6407 Evaluate side-chains 132 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0870 chunk 25 optimal weight: 0.0670 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7445 Z= 0.157 Angle : 0.620 9.060 10078 Z= 0.320 Chirality : 0.039 0.258 1108 Planarity : 0.003 0.045 1259 Dihedral : 4.022 27.358 975 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.13 % Allowed : 0.89 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 869 helix: 2.06 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.98 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 321 HIS 0.017 0.001 HIS B 79 PHE 0.014 0.001 PHE B 214 TYR 0.009 0.001 TYR B 117 ARG 0.005 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ASN cc_start: 0.8761 (m-40) cc_final: 0.8459 (m-40) REVERT: B 117 TYR cc_start: 0.8843 (m-10) cc_final: 0.8599 (m-80) REVERT: B 127 ASP cc_start: 0.8872 (t70) cc_final: 0.8437 (t0) REVERT: A 72 LYS cc_start: 0.9219 (mttt) cc_final: 0.8693 (mmtm) REVERT: A 152 MET cc_start: 0.8188 (tpt) cc_final: 0.7126 (tpt) REVERT: A 215 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8725 (ttp-110) REVERT: A 321 ARG cc_start: 0.8401 (ptt90) cc_final: 0.8093 (tmm160) REVERT: A 418 ASP cc_start: 0.9182 (m-30) cc_final: 0.8928 (m-30) REVERT: A 441 MET cc_start: 0.8995 (tmm) cc_final: 0.8618 (tmm) REVERT: A 510 LYS cc_start: 0.9021 (tttt) cc_final: 0.8314 (tmtt) REVERT: A 514 ASP cc_start: 0.8404 (m-30) cc_final: 0.8133 (m-30) REVERT: A 520 MET cc_start: 0.8570 (mmp) cc_final: 0.8288 (mmm) REVERT: A 609 MET cc_start: 0.8506 (ttt) cc_final: 0.8088 (tmm) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1831 time to fit residues: 41.3781 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 81 HIS B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7445 Z= 0.167 Angle : 0.630 10.546 10078 Z= 0.321 Chirality : 0.039 0.248 1108 Planarity : 0.003 0.046 1259 Dihedral : 4.029 24.236 975 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 869 helix: 2.11 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.93 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 321 HIS 0.004 0.001 HIS A 122 PHE 0.015 0.001 PHE B 214 TYR 0.015 0.001 TYR B 311 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 TYR cc_start: 0.8830 (m-10) cc_final: 0.8592 (m-80) REVERT: B 127 ASP cc_start: 0.8870 (t70) cc_final: 0.8537 (t0) REVERT: B 189 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: B 192 GLU cc_start: 0.9437 (tp30) cc_final: 0.9187 (tp30) REVERT: B 215 TYR cc_start: 0.4177 (t80) cc_final: 0.3896 (t80) REVERT: A 72 LYS cc_start: 0.9262 (mttt) cc_final: 0.8733 (mmtm) REVERT: A 152 MET cc_start: 0.7608 (tpt) cc_final: 0.6894 (tpt) REVERT: A 215 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8711 (ttp-110) REVERT: A 217 ILE cc_start: 0.9513 (mt) cc_final: 0.9222 (tp) REVERT: A 321 ARG cc_start: 0.8382 (ptt90) cc_final: 0.7850 (tmm-80) REVERT: A 418 ASP cc_start: 0.9206 (m-30) cc_final: 0.8990 (m-30) REVERT: A 441 MET cc_start: 0.9049 (tmm) cc_final: 0.8670 (tmm) REVERT: A 510 LYS cc_start: 0.9018 (tttt) cc_final: 0.8296 (tmtt) REVERT: A 514 ASP cc_start: 0.8428 (m-30) cc_final: 0.8144 (m-30) REVERT: A 609 MET cc_start: 0.8500 (ttt) cc_final: 0.8070 (tmm) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1869 time to fit residues: 40.6522 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 69 optimal weight: 0.0060 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7445 Z= 0.150 Angle : 0.627 9.993 10078 Z= 0.318 Chirality : 0.038 0.224 1108 Planarity : 0.003 0.047 1259 Dihedral : 3.944 23.464 975 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.29), residues: 869 helix: 2.18 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -2.00 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP B 321 HIS 0.012 0.001 HIS B 79 PHE 0.028 0.001 PHE B 83 TYR 0.013 0.001 TYR B 117 ARG 0.006 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8803 (t70) cc_final: 0.8272 (t0) REVERT: B 130 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8671 (tm-30) REVERT: B 189 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8809 (mm-40) REVERT: B 193 PHE cc_start: 0.9081 (m-80) cc_final: 0.8870 (m-80) REVERT: A 72 LYS cc_start: 0.9286 (mttt) cc_final: 0.8773 (mmtm) REVERT: A 91 GLU cc_start: 0.8865 (pt0) cc_final: 0.8653 (tp30) REVERT: A 152 MET cc_start: 0.7415 (tpt) cc_final: 0.6709 (tpt) REVERT: A 215 ARG cc_start: 0.9048 (ttm110) cc_final: 0.8710 (ttp80) REVERT: A 217 ILE cc_start: 0.9527 (mt) cc_final: 0.9234 (tp) REVERT: A 321 ARG cc_start: 0.8399 (ptt90) cc_final: 0.8108 (tmm160) REVERT: A 349 LEU cc_start: 0.9569 (tp) cc_final: 0.9369 (tp) REVERT: A 418 ASP cc_start: 0.9232 (m-30) cc_final: 0.8951 (m-30) REVERT: A 441 MET cc_start: 0.9010 (tmm) cc_final: 0.8644 (tmm) REVERT: A 510 LYS cc_start: 0.8911 (tttt) cc_final: 0.8161 (tmtt) REVERT: A 514 ASP cc_start: 0.8411 (m-30) cc_final: 0.8104 (m-30) REVERT: A 609 MET cc_start: 0.8407 (ttt) cc_final: 0.8003 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1932 time to fit residues: 45.0493 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 0.0010 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082383 restraints weight = 22828.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082364 restraints weight = 13006.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083257 restraints weight = 10180.825| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7445 Z= 0.165 Angle : 0.646 10.327 10078 Z= 0.331 Chirality : 0.040 0.225 1108 Planarity : 0.004 0.091 1259 Dihedral : 3.955 24.604 975 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.29), residues: 869 helix: 2.20 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 321 HIS 0.006 0.001 HIS A 122 PHE 0.023 0.001 PHE B 193 TYR 0.036 0.001 TYR B 117 ARG 0.015 0.001 ARG A 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.18 seconds wall clock time: 33 minutes 27.84 seconds (2007.84 seconds total)